data_4G5O
#
_model_server_result.job_id            ui-HhXYg9xK31LcWJh5ghg 
_model_server_result.datetime_utc      '2024-11-08 17:02:29' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          4g5o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":401}' 
#
_entry.id    4G5O 
#
_exptl.entry_id    4G5O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            4G5O 
_cell.length_a            207.326 
_cell.length_b            207.326 
_cell.length_c            236.545 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4G5O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I,J,K,L,M,N,O,HA 1 1 
B,F,P,Q,R,S,T,IA,LA 2 1 
C,G,U,V,W,X,Y,Z,JA,MA 3 1 
D,H,AA,BA,CA,DA,EA,FA,GA,KA 4 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 I N N 
? 3 P N N 
? 3 U N N 
? 3 AA N N 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PB O1B GDP doub 103 n n 
PB O2B GDP sing 104 n n 
PB O3B GDP sing 105 n n 
PB O3A GDP sing 106 n n 
O2B HOB2 GDP sing 107 n n 
O3B HOB3 GDP sing 108 n n 
O3A PA GDP sing 109 n n 
PA O1A GDP doub 110 n n 
PA O2A GDP sing 111 n n 
PA O5' GDP sing 112 n n 
O2A HOA2 GDP sing 113 n n 
O5' C5' GDP sing 114 n n 
C5' C4' GDP sing 115 n n 
C5' H5' GDP sing 116 n n 
C5' "H5''" GDP sing 117 n n 
C4' O4' GDP sing 118 n n 
C4' C3' GDP sing 119 n n 
C4' H4' GDP sing 120 n n 
O4' C1' GDP sing 121 n n 
C3' O3' GDP sing 122 n n 
C3' C2' GDP sing 123 n n 
C3' H3' GDP sing 124 n n 
O3' HO3' GDP sing 125 n n 
C2' O2' GDP sing 126 n n 
C2' C1' GDP sing 127 n n 
C2' H2' GDP sing 128 n n 
O2' HO2' GDP sing 129 n n 
C1' N9 GDP sing 130 n n 
C1' H1' GDP sing 131 n n 
N9 C8 GDP sing 132 n y 
N9 C4 GDP sing 133 n y 
C8 N7 GDP doub 134 n y 
C8 H8 GDP sing 135 n n 
N7 C5 GDP sing 136 n y 
C5 C6 GDP sing 137 n n 
C5 C4 GDP doub 138 n y 
C6 O6 GDP doub 139 n n 
C6 N1 GDP sing 140 n n 
N1 C2 GDP sing 141 n n 
N1 HN1 GDP sing 142 n n 
C2 N2 GDP sing 143 n n 
C2 N3 GDP doub 144 n n 
N2 HN21 GDP sing 145 n n 
N2 HN22 GDP sing 146 n n 
N3 C4 GDP sing 147 n n 
#
_atom_sites.entry_id                     4G5O 
_atom_sites.fract_transf_matrix[1][1]    0.004823 
_atom_sites.fract_transf_matrix[1][2]    0.002785 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005569 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.004228 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
I 3 GDP A 1 401 1 GDP GDP . 
J 4 CIT A 1 402 2 CIT CIT . 
K 4 CIT A 1 403 4 CIT CIT . 
L 5 SO4 A 1 404 3 SO4 SO4 . 
M 5 SO4 A 1 405 5 SO4 SO4 . 
N 5 SO4 A 1 406 7 SO4 SO4 . 
O 5 SO4 A 1 407 16 SO4 SO4 . 
P 3 GDP B 1 401 2 GDP GDP . 
Q 5 SO4 B 1 402 1 SO4 SO4 . 
R 5 SO4 B 1 403 4 SO4 SO4 . 
S 5 SO4 B 1 404 8 SO4 SO4 . 
T 5 SO4 B 1 405 18 SO4 SO4 . 
U 3 GDP C 1 401 3 GDP GDP . 
V 4 CIT C 1 402 1 CIT CIT . 
W 5 SO4 C 1 403 2 SO4 SO4 . 
X 5 SO4 C 1 404 6 SO4 SO4 . 
Y 5 SO4 C 1 405 11 SO4 SO4 . 
Z 5 SO4 C 1 406 13 SO4 SO4 . 
AA 3 GDP D 1 401 4 GDP GDP . 
BA 4 CIT D 1 402 3 CIT CIT . 
CA 5 SO4 D 1 403 9 SO4 SO4 . 
DA 5 SO4 D 1 404 10 SO4 SO4 . 
EA 5 SO4 D 1 405 15 SO4 SO4 . 
FA 5 SO4 D 1 406 17 SO4 SO4 . 
GA 5 SO4 D 1 407 19 SO4 SO4 . 
HA 6 HOH A 1 501 14 HOH HOH . 
HA 6 HOH A 2 502 37 HOH HOH . 
IA 6 HOH B 1 501 11 HOH HOH . 
JA 6 HOH C 1 501 2 HOH HOH . 
JA 6 HOH C 2 502 8 HOH HOH . 
JA 6 HOH C 3 503 25 HOH HOH . 
JA 6 HOH C 4 504 34 HOH HOH . 
KA 6 HOH D 1 501 5 HOH HOH . 
KA 6 HOH D 2 502 7 HOH HOH . 
KA 6 HOH D 3 503 12 HOH HOH . 
LA 6 HOH F 1 701 10 HOH HOH . 
MA 6 HOH G 1 701 16 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PB GDP . . . AA 3 43.447 -101.576 -19.428 1 48.01 ? PB GDP 401 D 1 
HETATM 2 O O1B GDP . . . AA 3 41.947 -101.739 -19.331 1 51.6 ? O1B GDP 401 D 1 
HETATM 3 O O2B GDP . . . AA 3 44.156 -101.95 -18.148 1 48.14 ? O2B GDP 401 D 1 
HETATM 4 O O3B GDP . . . AA 3 44.008 -102.221 -20.673 1 46.94 ? O3B GDP 401 D 1 
HETATM 5 O O3A GDP . . . AA 3 43.627 -99.974 -19.551 1 43.83 ? O3A GDP 401 D 1 
HETATM 6 P PA GDP . . . AA 3 44.044 -99.318 -20.953 1 45.46 ? PA GDP 401 D 1 
HETATM 7 O O1A GDP . . . AA 3 43.036 -99.679 -22.011 1 47.71 ? O1A GDP 401 D 1 
HETATM 8 O O2A GDP . . . AA 3 45.498 -99.682 -21.191 1 46.63 ? O2A GDP 401 D 1 
HETATM 9 O O5' GDP . . . AA 3 43.923 -97.731 -20.75 1 45.25 ? O5' GDP 401 D 1 
HETATM 10 C C5' GDP . . . AA 3 42.733 -97.15 -20.236 1 47.8 ? C5' GDP 401 D 1 
HETATM 11 C C4' GDP . . . AA 3 42.537 -95.766 -20.858 1 50.53 ? C4' GDP 401 D 1 
HETATM 12 O O4' GDP . . . AA 3 43.306 -94.739 -20.211 1 48.45 ? O4' GDP 401 D 1 
HETATM 13 C C3' GDP . . . AA 3 42.905 -95.679 -22.328 1 50.77 ? C3' GDP 401 D 1 
HETATM 14 O O3' GDP . . . AA 3 41.98 -94.706 -22.854 1 54.1 ? O3' GDP 401 D 1 
HETATM 15 C C2' GDP . . . AA 3 44.308 -95.08 -22.356 1 51.5 ? C2' GDP 401 D 1 
HETATM 16 O O2' GDP . . . AA 3 44.574 -94.34 -23.564 1 48.86 ? O2' GDP 401 D 1 
HETATM 17 C C1' GDP . . . AA 3 44.331 -94.216 -21.094 1 50.18 ? C1' GDP 401 D 1 
HETATM 18 N N9 GDP . . . AA 3 45.578 -94.236 -20.278 1 49.12 ? N9 GDP 401 D 1 
HETATM 19 C C8 GDP . . . AA 3 46.274 -95.318 -19.832 1 47.93 ? C8 GDP 401 D 1 
HETATM 20 N N7 GDP . . . AA 3 47.333 -94.94 -19.056 1 46.02 ? N7 GDP 401 D 1 
HETATM 21 C C5 GDP . . . AA 3 47.295 -93.592 -18.982 1 44.98 ? C5 GDP 401 D 1 
HETATM 22 C C6 GDP . . . AA 3 48.088 -92.533 -18.339 1 43.75 ? C6 GDP 401 D 1 
HETATM 23 O O6 GDP . . . AA 3 49.073 -92.853 -17.654 1 44.49 ? O6 GDP 401 D 1 
HETATM 24 N N1 GDP . . . AA 3 47.724 -91.252 -18.508 1 42.28 ? N1 GDP 401 D 1 
HETATM 25 C C2 GDP . . . AA 3 46.658 -90.904 -19.247 1 41.44 ? C2 GDP 401 D 1 
HETATM 26 N N2 GDP . . . AA 3 46.301 -89.602 -19.385 1 39.17 ? N2 GDP 401 D 1 
HETATM 27 N N3 GDP . . . AA 3 45.897 -91.824 -19.866 1 43.69 ? N3 GDP 401 D 1 
HETATM 28 C C4 GDP . . . AA 3 46.152 -93.141 -19.778 1 45.39 ? C4 GDP 401 D 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           28 
#